Dear Greg,

When I read that you did not reproduce the problem,
I updated from rdkit-2016-03.1 to rdkit-2017-03.1
and this solved the problem.

Thank you !

Jean-Marc


Le 19/06/2017 à 11:04, Greg Landrum a écrit :
Hi Jean-Marc,

I can't reproduce that:

    In [2]: m = Chem.MolFromSmiles('CN1CCC[C@H]1c1cccnc1')

    In [3]: Chem.MolToSmiles(m,isomericSmiles=True)
    Out[3]: 'CN1CCC[C@H]1c1cccnc1'

    In [4]: Chem.MolToSmiles(m,isomericSmiles=True,allHsExplicit=True)
    Out[4]: '[CH3][N]1[CH2][CH2][CH2][C@H]1[c]1[cH][cH][cH][n][cH]1'


Can you send some sample code that shows the problem?

-greg


On Mon, Jun 19, 2017 at 10:59 AM, Jean-Marc Nuzillard <jm.nuzill...@univ-reims.fr <mailto:jm.nuzill...@univ-reims.fr>> wrote:

    Dear All,

    Chem.MolToSmiles(m, isomericSmiles=True, allHsExplicit=False) with
    m being nicotine downloaded from PubChem returns
    CN1CCC[C@H]1c1cccnc1 , which is consistent with the structure of
    nicotine.
    Chem.MolToSmiles(m, isomericSmiles=True, allHsExplicit=True) returns
    [CH3][N]1[CH2][CH2][CH2][CH]1[c]1[cH][cH][cH][n][cH]1 in which
    chirality has disappeared.
    Would it be possible to get H count and chirality?

    All the best,

    Jean-Marc

-- Jean-Marc Nuzillard
    Directeur de Recherches au CNRS

    Institut de Chimie Moléculaire de Reims
    CNRS UMR 7312
    Moulin de la Housse
    CPCBAI, Bâtiment 18
    BP 1039
    51687 REIMS Cedex 2
    France

    Tel : 03 26 91 82 10
    Fax : 03 26 91 31 66
    http://www.univ-reims.fr/ICMR
    http://eos.univ-reims.fr/LSD/ISgroup.html
    <http://eos.univ-reims.fr/LSD/ISgroup.html>

    http://www.univ-reims.fr/LSD/
    http://www.univ-reims.fr/LSD/JmnSoft/
    <http://www.univ-reims.fr/LSD/JmnSoft/>


    
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--
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

Tel : 03 26 91 82 10
Fax : 03 26 91 31 66
http://www.univ-reims.fr/ICMR
http://eos.univ-reims.fr/LSD/ISgroup.html

http://www.univ-reims.fr/LSD/
http://www.univ-reims.fr/LSD/JmnSoft/

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